Magnesium in PDB 3oxm: Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Protein crystallography data
The structure of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked, PDB code: 3oxm
was solved by
L.Huang,
A.Serganov,
D.J.Patel,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
20.00 /
2.95
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.783,
83.783,
200.066,
90.00,
90.00,
120.00
|
R / Rfree (%)
|
20 /
22.5
|
Other elements in 3oxm:
The structure of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked also contains other interesting chemical elements:
Magnesium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
20;
Page 3, Binding sites: 21 -
27;
Binding sites:
The binding sites of Magnesium atom in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
(pdb code 3oxm). This binding sites where shown within
5.0 Angstroms radius around Magnesium atom.
In total 27 binding sites of Magnesium where determined in the
Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked, PDB code: 3oxm:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Magnesium binding site 1 out
of 27 in 3oxm
Go back to
Magnesium Binding Sites List in 3oxm
Magnesium binding site 1 out
of 27 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 1 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg101
b:55.2
occ:1.00
|
OP2
|
A:G35
|
2.1
|
67.1
|
1.0
|
OP1
|
A:A34
|
2.1
|
60.9
|
1.0
|
O
|
A:HOH140
|
2.2
|
26.8
|
1.0
|
O
|
A:HOH111
|
2.2
|
26.9
|
1.0
|
O
|
A:HOH139
|
2.2
|
27.4
|
1.0
|
O
|
A:HOH138
|
2.2
|
27.4
|
1.0
|
P
|
A:G35
|
3.5
|
68.1
|
1.0
|
P
|
A:A34
|
3.6
|
61.3
|
1.0
|
CA
|
A:GLY89
|
4.1
|
60.3
|
1.0
|
O5'
|
A:A34
|
4.1
|
62.5
|
1.0
|
OP1
|
A:G35
|
4.2
|
68.3
|
1.0
|
O5'
|
A:G35
|
4.3
|
69.2
|
1.0
|
C4'
|
A:A33
|
4.3
|
57.4
|
1.0
|
O3'
|
A:A33
|
4.4
|
59.7
|
1.0
|
O3'
|
A:A34
|
4.5
|
67.6
|
1.0
|
C5'
|
A:A34
|
4.5
|
63.5
|
1.0
|
OP2
|
A:A34
|
4.6
|
61.7
|
1.0
|
N7
|
A:G35
|
4.7
|
67.4
|
1.0
|
N7
|
A:G36
|
4.7
|
63.5
|
1.0
|
C5'
|
A:A33
|
4.8
|
56.2
|
1.0
|
C3'
|
A:A33
|
4.8
|
58.1
|
1.0
|
N
|
A:GLY89
|
4.9
|
61.2
|
1.0
|
C3'
|
A:A34
|
4.9
|
66.7
|
1.0
|
C8
|
A:G35
|
4.9
|
68.0
|
1.0
|
O2'
|
A:A81
|
5.0
|
58.7
|
1.0
|
|
Magnesium binding site 2 out
of 27 in 3oxm
Go back to
Magnesium Binding Sites List in 3oxm
Magnesium binding site 2 out
of 27 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 2 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg102
b:82.4
occ:1.00
|
O
|
A:HOH142
|
2.2
|
57.9
|
1.0
|
O
|
A:HOH115
|
2.2
|
57.5
|
1.0
|
O
|
A:HOH141
|
2.2
|
57.8
|
1.0
|
OP2
|
A:A33
|
2.2
|
54.1
|
1.0
|
O2'
|
A:G32
|
2.4
|
54.3
|
1.0
|
OP2
|
A:C66
|
2.7
|
54.7
|
1.0
|
C2'
|
A:G32
|
3.2
|
53.8
|
1.0
|
O
|
A:GLY89
|
3.5
|
59.4
|
1.0
|
P
|
A:A33
|
3.6
|
54.2
|
1.0
|
C3'
|
A:G32
|
3.6
|
53.4
|
1.0
|
O3'
|
A:G32
|
3.9
|
53.8
|
1.0
|
O4
|
A:U69
|
4.1
|
63.0
|
1.0
|
P
|
A:C66
|
4.1
|
54.7
|
1.0
|
C5'
|
A:A33
|
4.5
|
56.2
|
1.0
|
O5'
|
A:A33
|
4.5
|
55.0
|
1.0
|
OP1
|
A:A33
|
4.6
|
54.1
|
1.0
|
C
|
A:GLY89
|
4.6
|
59.8
|
1.0
|
C1'
|
A:G32
|
4.6
|
54.0
|
1.0
|
C5
|
A:U67
|
4.6
|
54.7
|
1.0
|
O4
|
A:U67
|
4.7
|
56.0
|
1.0
|
OP2
|
A:U67
|
4.8
|
51.7
|
1.0
|
N4
|
A:C68
|
4.8
|
55.9
|
1.0
|
O3'
|
A:A65
|
4.9
|
55.9
|
1.0
|
OXT
|
A:GLY89
|
4.9
|
59.9
|
1.0
|
OP1
|
A:C66
|
5.0
|
54.6
|
1.0
|
O5'
|
A:C66
|
5.0
|
53.8
|
1.0
|
|
Magnesium binding site 3 out
of 27 in 3oxm
Go back to
Magnesium Binding Sites List in 3oxm
Magnesium binding site 3 out
of 27 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 3 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg103
b:89.7
occ:1.00
|
OP2
|
A:A75
|
2.4
|
58.3
|
1.0
|
OP1
|
A:A22
|
2.8
|
57.4
|
1.0
|
O3'
|
A:A21
|
3.7
|
56.5
|
1.0
|
P
|
A:A22
|
3.9
|
57.5
|
1.0
|
P
|
A:A75
|
3.9
|
57.9
|
1.0
|
N7
|
A:A75
|
4.1
|
58.0
|
1.0
|
O5'
|
A:A75
|
4.4
|
57.5
|
1.0
|
C8
|
A:A75
|
4.4
|
57.8
|
1.0
|
O3'
|
A:C74
|
4.8
|
58.0
|
1.0
|
O4'
|
A:A13
|
4.8
|
54.5
|
1.0
|
OP2
|
A:A22
|
4.9
|
58.4
|
1.0
|
OP1
|
A:A75
|
4.9
|
57.5
|
1.0
|
C3'
|
A:C74
|
5.0
|
57.8
|
1.0
|
OP1
|
A:C74
|
5.0
|
59.6
|
1.0
|
O5'
|
A:A22
|
5.0
|
57.5
|
1.0
|
|
Magnesium binding site 4 out
of 27 in 3oxm
Go back to
Magnesium Binding Sites List in 3oxm
Magnesium binding site 4 out
of 27 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 4 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg104
b:82.9
occ:1.00
|
OP1
|
A:A75
|
2.2
|
57.5
|
1.0
|
OP2
|
A:A76
|
2.4
|
56.9
|
1.0
|
OP1
|
A:C74
|
3.2
|
59.6
|
1.0
|
P
|
A:A75
|
3.5
|
57.9
|
1.0
|
P
|
A:A76
|
3.8
|
56.9
|
1.0
|
N6
|
A:A77
|
4.0
|
62.7
|
1.0
|
C5'
|
A:C74
|
4.0
|
58.0
|
1.0
|
N6
|
A:A78
|
4.1
|
60.0
|
1.0
|
N7
|
A:A77
|
4.1
|
61.8
|
1.0
|
OP2
|
A:A75
|
4.2
|
58.3
|
1.0
|
N7
|
A:A76
|
4.2
|
59.0
|
1.0
|
O5'
|
A:A75
|
4.3
|
57.5
|
1.0
|
O5'
|
A:A76
|
4.4
|
57.8
|
1.0
|
P
|
A:C74
|
4.5
|
59.5
|
1.0
|
C8
|
A:A76
|
4.6
|
58.9
|
1.0
|
O5'
|
A:C74
|
4.6
|
59.2
|
1.0
|
O3'
|
A:C74
|
4.6
|
58.0
|
1.0
|
O3'
|
A:A75
|
4.7
|
57.0
|
1.0
|
OP1
|
A:A76
|
4.7
|
56.9
|
1.0
|
C3'
|
A:A75
|
4.8
|
57.1
|
1.0
|
C6
|
A:A78
|
4.8
|
60.1
|
1.0
|
C5
|
A:A77
|
4.9
|
62.0
|
1.0
|
C6
|
A:A77
|
4.9
|
62.3
|
1.0
|
C4'
|
A:C74
|
4.9
|
57.5
|
1.0
|
C5'
|
A:A75
|
4.9
|
57.1
|
1.0
|
|
Magnesium binding site 5 out
of 27 in 3oxm
Go back to
Magnesium Binding Sites List in 3oxm
Magnesium binding site 5 out
of 27 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 5 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg106
b:88.8
occ:1.00
|
OP1
|
A:A33
|
3.3
|
54.1
|
1.0
|
OP1
|
A:C66
|
3.7
|
54.6
|
1.0
|
P
|
A:A33
|
4.6
|
54.2
|
1.0
|
OP1
|
B:A33
|
4.6
|
48.7
|
1.0
|
|
Magnesium binding site 6 out
of 27 in 3oxm
Go back to
Magnesium Binding Sites List in 3oxm
Magnesium binding site 6 out
of 27 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 6 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg107
b:83.4
occ:1.00
|
OP1
|
B:G10
|
4.3
|
46.1
|
1.0
|
OP1
|
A:U67
|
4.4
|
51.5
|
1.0
|
OP2
|
A:G32
|
4.4
|
54.2
|
1.0
|
OP2
|
A:U67
|
4.7
|
51.7
|
1.0
|
OP2
|
A:C68
|
4.9
|
56.4
|
1.0
|
O3'
|
B:A9
|
5.0
|
46.1
|
1.0
|
|
Magnesium binding site 7 out
of 27 in 3oxm
Go back to
Magnesium Binding Sites List in 3oxm
Magnesium binding site 7 out
of 27 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 7 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg108
b:75.9
occ:1.00
|
OP1
|
B:U67
|
4.3
|
55.6
|
1.0
|
OP2
|
B:G32
|
4.3
|
46.5
|
1.0
|
OP2
|
B:C68
|
4.6
|
57.0
|
1.0
|
OP2
|
B:U67
|
4.8
|
55.2
|
1.0
|
OP1
|
A:G10
|
4.8
|
52.0
|
1.0
|
P
|
B:U67
|
5.0
|
55.5
|
1.0
|
|
Magnesium binding site 8 out
of 27 in 3oxm
Go back to
Magnesium Binding Sites List in 3oxm
Magnesium binding site 8 out
of 27 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 8 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Mg109
b:0.7
occ:1.00
|
O
|
A:HOH121
|
2.2
|
70.0
|
1.0
|
O
|
A:HOH120
|
2.2
|
69.8
|
1.0
|
O
|
A:HOH123
|
2.2
|
69.9
|
1.0
|
O
|
A:HOH143
|
2.2
|
69.9
|
1.0
|
O
|
A:HOH119
|
2.2
|
70.0
|
1.0
|
O
|
A:HOH122
|
2.2
|
70.1
|
1.0
|
OP2
|
A:A37
|
4.0
|
69.4
|
1.0
|
OP2
|
A:A64
|
4.2
|
56.1
|
1.0
|
N7
|
A:A37
|
4.5
|
61.1
|
1.0
|
OP1
|
A:A64
|
4.7
|
57.4
|
1.0
|
|
Magnesium binding site 9 out
of 27 in 3oxm
Go back to
Magnesium Binding Sites List in 3oxm
Magnesium binding site 9 out
of 27 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 9 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg110
b:89.3
occ:1.00
|
OP2
|
B:A76
|
2.1
|
64.2
|
1.0
|
O
|
B:HOH106
|
2.2
|
62.9
|
1.0
|
O
|
B:HOH107
|
2.2
|
63.3
|
1.0
|
O
|
B:HOH116
|
2.2
|
63.3
|
1.0
|
OP1
|
B:C74
|
2.2
|
54.7
|
1.0
|
OP1
|
B:A75
|
2.3
|
58.4
|
1.0
|
P
|
B:A75
|
3.4
|
58.3
|
1.0
|
O5'
|
B:A75
|
3.5
|
59.0
|
1.0
|
P
|
B:C74
|
3.5
|
54.7
|
1.0
|
P
|
B:A76
|
3.6
|
64.3
|
1.0
|
C5'
|
B:C74
|
3.7
|
54.1
|
1.0
|
O5'
|
B:C74
|
3.9
|
54.5
|
1.0
|
OP1
|
B:A76
|
4.3
|
64.3
|
1.0
|
N6
|
B:A78
|
4.3
|
57.4
|
1.0
|
O3'
|
B:C74
|
4.3
|
56.5
|
1.0
|
O5'
|
B:A76
|
4.4
|
65.0
|
1.0
|
O3'
|
B:A75
|
4.5
|
63.7
|
1.0
|
O3'
|
B:G73
|
4.5
|
54.2
|
1.0
|
N7
|
B:A77
|
4.5
|
63.0
|
1.0
|
N6
|
B:A77
|
4.5
|
63.1
|
1.0
|
N7
|
B:A76
|
4.5
|
65.3
|
1.0
|
OP2
|
B:C74
|
4.6
|
55.1
|
1.0
|
C4'
|
B:C74
|
4.6
|
53.7
|
1.0
|
OP2
|
B:A75
|
4.7
|
59.1
|
1.0
|
C3'
|
B:A75
|
4.7
|
63.3
|
1.0
|
C3'
|
B:C74
|
4.8
|
54.2
|
1.0
|
C8
|
B:A76
|
4.8
|
65.2
|
1.0
|
C5'
|
B:A75
|
4.9
|
60.3
|
1.0
|
|
Magnesium binding site 10 out
of 27 in 3oxm
Go back to
Magnesium Binding Sites List in 3oxm
Magnesium binding site 10 out
of 27 in the Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked
Mono view
Stereo pair view
|
A full contact list of Magnesium with other atoms in the Mg binding
site number 10 of Crystal Structure of Glycine Riboswitch, Tl-Acetate Soaked within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Mg111
b:80.2
occ:1.00
|
OP2
|
B:A33
|
2.1
|
49.0
|
1.0
|
O
|
B:HOH109
|
2.2
|
54.4
|
1.0
|
O
|
B:HOH117
|
2.2
|
54.9
|
1.0
|
O
|
B:HOH118
|
2.2
|
54.4
|
1.0
|
O2'
|
B:G32
|
2.5
|
50.2
|
1.0
|
OP2
|
B:C66
|
2.6
|
59.1
|
1.0
|
O
|
B:GLY89
|
3.4
|
64.2
|
1.0
|
P
|
B:A33
|
3.5
|
48.8
|
1.0
|
C2'
|
B:G32
|
3.6
|
49.1
|
1.0
|
C3'
|
B:G32
|
3.9
|
48.3
|
1.0
|
P
|
B:C66
|
4.0
|
59.9
|
1.0
|
O3'
|
B:G32
|
4.0
|
48.4
|
1.0
|
O4
|
B:U67
|
4.1
|
55.8
|
1.0
|
C5
|
B:U67
|
4.1
|
55.1
|
1.0
|
C5'
|
B:A65
|
4.3
|
57.2
|
1.0
|
C4'
|
B:A65
|
4.4
|
57.8
|
1.0
|
C
|
B:GLY89
|
4.4
|
64.3
|
1.0
|
OP1
|
B:A33
|
4.4
|
48.7
|
1.0
|
C4
|
B:U67
|
4.4
|
55.6
|
1.0
|
C5'
|
B:A33
|
4.4
|
49.8
|
1.0
|
O4
|
B:U69
|
4.5
|
56.8
|
1.0
|
O5'
|
B:A33
|
4.5
|
49.1
|
1.0
|
O3'
|
B:A65
|
4.5
|
59.7
|
1.0
|
OXT
|
B:GLY89
|
4.7
|
64.0
|
1.0
|
N4
|
B:C68
|
4.8
|
57.3
|
1.0
|
OP2
|
B:U67
|
4.9
|
55.2
|
1.0
|
C1'
|
B:G32
|
4.9
|
49.4
|
1.0
|
OP1
|
B:C66
|
4.9
|
59.3
|
1.0
|
O5'
|
B:C66
|
4.9
|
58.9
|
1.0
|
|
Reference:
L.Huang,
A.Serganov,
D.J.Patel.
Structural Insights Into Ligand Recognition By A Sensing Domain of the Cooperative Glycine Riboswitch. Mol.Cell V. 40 774 2010.
ISSN: ISSN 1097-2765
PubMed: 21145485
DOI: 10.1016/J.MOLCEL.2010.11.026
Page generated: Thu Aug 15 08:49:59 2024
|